Oh yes, I should have specified - I have a few versions of R downloaded!
Output of that command is:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
distribution: 10.15.6
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/liuj10/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 17 2020
: AFNI_20.2.18 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.18, macos_10.12_local, Sep 17 2020
which python : /Users/liuj10/opt/anaconda2/bin/python
python version : 2.7.16
which R : /Users/liuj10/opt/anaconda2/bin/R
R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/liuj10/abin/afni)
R : 2
/Users/liuj10/opt/anaconda2/bin/R
/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R
python : 2
/Users/liuj10/opt/anaconda2/bin/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
python2 : 2
/Users/liuj10/opt/anaconda2/bin/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
python3 : 1 (/usr/bin/python3)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/liuj10/abin/R_io.so':
dlopen(/Users/liuj10/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/liuj10/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /Users/liuj10/opt/anaconda2/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /Users/liuj10/opt/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc
-------------------------------- env vars --------------------------------
PATH = /usr/local/ANTs/bin/:/Users/liuj10/opt/anaconda2/bin:/Users/liuj10/opt/anaconda2/condabin:/usr/local/fsl/bin:/usr/local/DTIPrepTools-0.1.1-Linux/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MATLAB_R2019a.app/bin:/opt/X11/bin:/Users/liuj10/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/liuj10/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.5.1
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.64.3/lib/libglib-2.0.dylib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'bash'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* consider installing gcc under homebrew
Thanks!
-Janelle
Edited 1 time(s). Last edit at 09/23/2020 02:02PM by janelleliu.
